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      The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Summary: RNA silencing is a complex, highly conserved mechanism mediated by small RNAs (sRNAs), such as microRNAs (miRNAs), that is known to be involved in a diverse set of biological functions including development, pathogen control, genome maintenance and response to environmental change. Advances in next generation sequencing technologies are producing increasingly large numbers of sRNA reads per sample at a fraction of the cost of previous methods. However, many bioinformatics tools do not scale accordingly, are cumbersome, or require extensive support from bioinformatics experts. Therefore, researchers need user-friendly, robust tools, capable of not only processing large sRNA datasets in a reasonable time frame but also presenting the results in an intuitive fashion and visualizing sRNA genomic features. Herein, we present the UEA sRNA workbench, a suite of tools that is a successor to the web-based UEA sRNA Toolkit, but in downloadable format and with several enhanced and additional features.

          Availability: The program and help pages are available at http://srna-workbench.cmp.uea.ac.uk.

          Contact: vincent.moulton@ 123456cmp.uea.ac.uk

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          A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana.

          Ramya Rajagopalan, Hervé Vaucheret, Jerry Trejo … (2006)
          To better understand the diversity of small silencing RNAs expressed in plants, we employed high-throughput pyrosequencing to obtain 887,000 reads corresponding to Arabidopsis thaliana small RNAs. They represented 340,000 unique sequences, a substantially greater diversity than previously obtained in any species. Most of the small RNAs had the properties of heterochromatic small interfering RNAs (siRNAs) associated with DNA silencing in that they were preferentially 24 nucleotides long and mapped to intergenic regions. Their density was greatest in the proximal and distal pericentromeric regions, with only a slightly preferential propensity to match repetitive elements. Also present were 38 newly identified microRNAs (miRNAs) and dozens of other plausible candidates. One miRNA mapped within an intron of DICER-LIKE 1 (DCL1), suggesting a second homeostatic autoregulatory mechanism for DCL1 expression; another defined the phase for siRNAs deriving from a newly identified trans-acting siRNA gene (TAS4); and two depended on DCL4 rather than DCL1 for their accumulation, indicating a second pathway for miRNA biogenesis in plants. More generally, our results revealed the existence of a layer of miRNA-based control beyond that found previously that is evolutionarily much more fluid, employing many newly emergent and diverse miRNAs, each expressed in specialized tissues or at low levels under standard growth conditions.
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            Fast folding and comparison of RNA secondary structures

            I. Hofacker, W Fontana, P. Stadler … (1994)
            Article 0 comments Cited 437 times – based on 0 reviews     Review now
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              Specialization and evolution of endogenous small RNA pathways.

              Elisabeth Chapman, James Carrington (2007)
              The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.
              Article 0 comments Cited 170 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 1 August 2012
                Publication date (Electronic): 24 May 2012
                Publication date PMC-release: 24 May 2012
                Volume: 28
                Issue: 15
                Pages: 2059-2061
                Affiliations
                1School of Computing Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK 2Department of Genetics, Yale University, School of Medicine, 333 Cedar Street, New Haven CT 06520, USA 3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK and 4School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK
                Author notes
                * To whom correspondence should be addressed.

                Associate Editor: Ivo Hofacker

                Article
                Publisher ID: bts311
                DOI: 10.1093/bioinformatics/bts311
                PMC ID: 3400958
                PubMed ID: 22628521
                SO-VID: 252c17c8-ffc4-4198-9131-2ba35b9d823d
                Copyright © © The Author(s) 2012. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 10 February 2012
                Date revision received : 8 May 2012
                Date accepted : 22 May 2012
                Page count
                Pages: 3
                Categories
                Subject: Applications Note
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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